EP2078008A2 - Quinoline derivatives for modulating dna methylation - Google Patents

Quinoline derivatives for modulating dna methylation

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Publication number
EP2078008A2
EP2078008A2 EP07854027A EP07854027A EP2078008A2 EP 2078008 A2 EP2078008 A2 EP 2078008A2 EP 07854027 A EP07854027 A EP 07854027A EP 07854027 A EP07854027 A EP 07854027A EP 2078008 A2 EP2078008 A2 EP 2078008A2
Authority
EP
European Patent Office
Prior art keywords
arh
acid
meoh
mmol
amino
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP07854027A
Other languages
German (de)
English (en)
French (fr)
Inventor
Pasit Phiasivongsa
Sanjeev Redkar
Swarna Gamage
Darby Brooke
William Denny
David J. Bearss
Hariprasad Vankayalapati
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Astex Pharmaceuticals Inc
Original Assignee
Supergen Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Supergen Inc filed Critical Supergen Inc
Priority to EP10000636A priority Critical patent/EP2174938A1/en
Publication of EP2078008A2 publication Critical patent/EP2078008A2/en
Withdrawn legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
    • C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
    • C07D401/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings linked by a chain containing hetero atoms as chain links
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/711—Natural deoxyribonucleic acids, i.e. containing only 2'-deoxyriboses attached to adenine, guanine, cytosine or thymine and having 3'-5' phosphodiester links
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/16—Drugs for disorders of the alimentary tract or the digestive system for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
    • A61P7/06—Antianaemics

Definitions

  • the present invention relates to compounds, compositions, formulations, kits, methods of use, and manufacture of quinoline derivatives, and more particularly to 4-anilinoquinoline derivatives as inhibitors of DNA methylation enzymes, modulators of DNA methylation and therapeutic agents for preventing or treating diseases associated with aberrant DNA methylation such as cancer and hematological malignancy.
  • Methylation at the C-5 position of cytosine residues in 5'-m 5 CpG- 3' sequences plays a major role in gene expression by the silencing of genes (Smith, A. F. A. Curr. Opin. Genet. Devel., 1999, 9, 657).
  • the major enzyme responsible for the maintenance of these methylation patterns during replication is the DNA methyltransferase DNMT1 (Siedlecki et al., Biochem.Biophys. Res. Comm., 2003, 306, 558).
  • DNA methylation is the cause of a number of inherited disease syndromes, and can also have a major role in the development of human cancer.
  • DNMT1 The most widely-explored inhibitors of DNMT1 are suicide inhibitors such as azacitidine (Vidaza®) and decitabine (Dacogen®), antimetabolites that incorporate into DNA in place of cytosine, and irreversibly trap the enzyme (Egger et al., Nature, 2004, 429, 457; Zhou et al., J. MoI. Biol., 2002, 327, 599). Both compounds are now used clinically for the treatment of myelodysplastic syndromes and lymphoproliferative diseases, but do possess considerable toxicity (Leone et al., Clin. Immunol., 2003, 109, 89). Presumably this is due to incorporation of 5-azacytidine into the DNA.
  • the present invention provides a compound of formula (I), or a physiologically acceptable salt or a phosphate prodrug, or a carboxylic acid or aminoacid ester prodrug thereof,
  • G 1 , G 2 , G 3 , and G 4 are each independently C, N, or N+ (where an R 6 - R 9 is attached to N);
  • G 5 and G 6 are each independently CH or N;
  • G 7 and G 8 are each independently CH, C (where an R 2 is attached to C), N, or N+ (where an R 2 is attached to N),
  • D 1 and D 2 are each separately CH, C (where R 3 attached to C), N, or N+ (where an R 3 is attached to N).
  • R 2 and R 3 are each independently H, NHR 4 , NR 4 R 5 , OR 4 , NO 2 or CH 2 R 4 , wherein R 4 and R 5 are defined as above, X may be H or CrC 6 alkyl optionally substituted with amino, hydroxyl or methoxy groups, or with one or more oxygen or nitrogen atoms as part of a cycloalkyl structure which may represent azetidine, pyrrolidine, piperidine, piperazine, or morpholine;
  • Z may be one of the groups Q1-Q43 represented in formula (II);
  • A is O or NR 4 , where R 4 is defined as above,
  • G 9 -G 13 are each independently C, N, or N+ (where an R 10 -R 13 is attached to N); but at least three of G 9 -G 13 are C; and
  • R 10 , R 11 , R 12 , R 13 , and R 14 are each separately H, halogen, alkyl, CF 3 , OCF 3 , CN, CONHR 4 , CONR 4 R 5 , SO 2 Me, SO 2 NHR 4 , SO 2 NR 4 R 5 , NHCOR 4 , NHR 4 , NR 4 R 5 , OR 4 , NO 2 or CH 2 R 4 , wherein R 4 and R 5 are as defined above.
  • the invention provides a compound of formula (ill), or a pharmaceutically acceptable salt, a phosphate prodrug, or a carboxylic acid or amino acid ester prodrug thereof, wherein
  • R 6 , R 7 , R 8 , and R 9 are each separately H, halogen, CF 3 , OCF 3 , CN, CONHR 4 , CONR 4 R 5 , SO 2 Me, SO 2 NHR 4 , SO 2 NR 4 R 5 , NHCOR 4 , NHR 4 , NR 4 R 5 , OR 4 , NO 2 or CH 2 R 4 , wherein R 4 and R 5 are each independently H, C 1 - C 6 alkyl, or cycloalkyl that is optionally substituted with one or more amino, hydroxyl or methoxy groups;
  • X is H, or C r C 6 alkyl that is optionally substituted with one or more amino, hydroxyl or methoxy groups;
  • G 7 and G 8 are each independently CH or N,
  • Di and D 2 are each independently CH or N, o, m and p represent positions of attachment of the moiety Z;
  • Z is one of the groups Q1-Q43represented in formula (II) above, wherein,
  • A is O or NR 4 , where R 4 is defined as above;
  • G 9- Gi 3 are each independently C, N, or N+ (where an R 10 -R 13 is attached to N), but at least three of G 9- G 13 are C,
  • R 10 , R 11 , R 12 , R 13 , and R 14 are each separately H, halogen, alkyl, CF 3 , OCF 3 , CN, CONHR 4 , CONR 4 R 5 , SO 2 Me, SO 2 NHR 4 , SO 2 NR 4 R 5 , NHCOR 4 , NHR 4 , NR 4 R 5 , OR 4 , NO 2 or CH 2 R 4 , and wherein R 4 and R 5 are as defined above.
  • the invention provides a method for treating or preventing a disease associated with aberrant DNA methylation, such as cancer, including the step of administering a compound of formula (I) or (III) or its salts or prodrugs, wherein R 2 -R 14 , G 1 -G1 3 , o, m, p, X, Y, Z, and A, are defined as above, respectively for each formula.
  • the subject in need of treatment or prevention of such a disease is in need of some reduction in the function/activity of the maintenance methylase DNMT1 , preferably at least 25%, more preferably at least 50%, and most preferably at least 75%, reduction of such function/activity. It is envisaged that at least 25% reduction in DNA methylase activity may be beneficial.
  • the method may also include co-administering one or more therapeutic agents and/or therapies. It is preferred that the method of therapy further includes the step of administering one or more chemotherapeutic or biologic therapeutic agents to, or radiating the subject before, during or after the administration of the compound of formula (I) or (III) or its salts or prodrugs as defined above.
  • While these compounds will typically be used in disease prevention or treatment of human subjects, they can be used to treat or prevent diseases in other mammals, such as warm blooded animal subjects (e.g., other primates, farm animals such as cattle, and sports animals and pets such as horses, dogs, and cats).
  • warm blooded animal subjects e.g., other primates, farm animals such as cattle, and sports animals and pets such as horses, dogs, and cats.
  • the present invention provides a pharmaceutical composition
  • a pharmaceutical composition comprising a compound of formula (I) or (III) or its salts or prodrugs as defined above, and a pharmaceutically acceptable excipient, adjuvant, carrier, buffer or stabiliser.
  • the present invention provides a method for synthesizing or manufacturing a compound of formula (I) or (III) or its salts or prodrugs as defined above. Examples of such a method are illustrated in Schemes 1-6 below.
  • the present invention provides a method for manufacture of a medicament comprising a compound of formula (I) or (III) or its salts or prodrugs as defined above for administration to a subject.
  • a compound of formula (I) or (III) or its salts or prodrugs as defined above for administration to a subject.
  • Examples of some preferred compound of Formula (I) is listed in Table 1 below, wherein R 2 , R 3 and R 4 are H, and A is NH,
  • pharmacologically acceptable salt used throughout the specification is to be taken as meaning any acid or base derived salt formed from hydrochloric, sulfuric, phosphoric, acetic, citric, oxalic, malonic, salicylic, malic, fumaric, succinic, ascorbic, maleic, methanesulfonic, isoethonic acids and the like and potassium carbonate sodium or potassium hydroxide ammonia, triethylamine, triethanolamine and the like.
  • the salt of the compound of formula (I) or (III) is formed with an acid selected from the group consisting of hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric acid, carboxylic, sulfonic, sulfo or phospho acids, acetic acid, propionic acid, glycolic acid, succinic acid, maleic acid, hydroxymaleic acid, methylmaleic acid, fumaric acid, malic acid, tartaric acid, lactic acid, oxalic acid, gluconic acid, glucaric acid, glucuronic acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, salicylic acid, 4-aminosalicylic acid, 2-phenoxybenzoic acid, 2-acetoxybenzoic acid, embonic acid, nicotinic acid, isonicotinic acid, amino acid, glutamic acid, aspartic acid, phenylacetic acid, methanesulfonic acid, e
  • an acid selected from the
  • Z is Q1 , Q2, Q3, Q4, Q9, or Q10.
  • the compound is a structure of formula (III), R 6 , R 7 , R 8 , and R 9 are each H; X is H; Y is CONH or NHCO; Z is Q2 or Q9; A is NH, and Z is attached at the m or p position.
  • the compound is a structure of formula (III), R 6 , R 7 , R 8 , and R 9 are each H; X is H; Y is CONH, Z is Q2; A is NH; and Z is attached at the p position.
  • the compound is a structure of formula (III), R 6 , R 7 , R 8 , and R 9 are each H; X is H; Y is CONH; Z is Q9; A is NH; and Z is attached at the p position.
  • the compound is a structure of formula (III), R 6 , R 7 , R 8 , and R 9 are each H; X is H; Y is CONH or NHCO; Z is Q2; A is NH, and Z is attached at the m position.
  • the compound is a structure of formula (III), R 6 , R 8 , and R 9 are each H; R 7 is NMe 2 ; X is H; Y is CONH or NHCO; Z is Q2; A is NH, and Z is attached at the m position.
  • the compound is a structure of formula (III), R 6 , R 8 , and R 9 are each H; R 7 is Cl; X is H; Y is CONH; Z is Q2; A is NH, and Z is attached at the p position.
  • the compound is a structure of formula (III), R 6 , R 7 , R 8 , and R 9 are separately H, F, or Cl.
  • One aspect of the invention is a pharmaceutical composition
  • a pharmaceutical composition comprising a compound, salt, or prodrug of formula (I) or (III) or its salts or prodrugs as defined above, and a pharmaceutically-acceptable carrier.
  • the compound, salt, or prodrug is in solid form.
  • the pharmaceutical composition is in an oral dosage form.
  • the pharmaceutical composition is in an injectable dosage form.
  • the pharmaceutical composition is in a topical dosage form.
  • One aspect of the invention is a method for inhibiting DNA methylation in a cell, comprising: contacting the cell with the compound of formula (I) or (III) or its salts or prodrugs as defined above, such that DNA methylation activity of the cell is inhibited.
  • One aspect of the invention is a method for inhibiting DNA methylation in a cell, comprising: contacting the cell with the compound of formula (I) or (III) or its salts or prodrugs as defined above, such that DNA methytransferase activity in the cell is inhibited.
  • the activity of DNA methyltransferase activity is inhibited via degradation of DNA methyltransferase DNMT1.
  • the step of contacting includes contacting the cell with a biologically effective amount of the compound of formula (I) or (III) or its salts or prodrugs as defined above, such that at least 50% of the activity of DNA methyltransferase DNMT1 in the cell is inhibited.
  • the step of contacting includes contacting the cell with a biologically effective amount of the compound of formula (I) or (III) or its salts or prodrugs as defined above, such that at least 25% of the activity of DNA methyltransferase DNMT1 in the cell is inhibited.
  • One aspect of the invention is a method for restoring activity of a DNA methylation-suppressed gene in a cell, comprising: contacting a cell with a biologically effective amount of the compound of formula (I) or (III) or its salts or prodrugs as defined above, such that activity of the DNA methylation- suppressed gene is elevated by at least 25% relative to that in the absence of the compound, salt, or prodrug.
  • the step of contacting includes contacting the cell with a biologically effective amount of the compound of formula (I) or (III) or its salts or prodrugs as defined above, such that transcriptional activity or levels of transcript of the DNA-methylation- suppressed gene is elevated by at least 25%.
  • the DNA methylation-suppressed gene is selected from the group consisting of 14-3-3 Sigma, ABL1 (P1 ), ABO, APC, AR (Androgen Receptor), BLT1 (Leukotriene B4 Receptor), BRCA1 , CALCA (Calcitonin), CASP8 (CASPASE 8), Caveolin 1 , CD44, CFTR, COX2, CSPG2 (Versican), CX26 (Connexin 26), Cyclin A1 , DBCCR1 , ECAD (E-cadherin), Endothelin Receptor B, EPHA3, EPO (Erythropoietin), ER (Estrogen Receptor), FHIT, GPC3 (Glypican 3), GST-pi, H19, H-Cadherin (CDH13), ⁇ -globin, HIC1 , hMLH1 , HOXA5, IGF2 (Insulin-Like Growth Factor II
  • One aspect of the invention is a method for treating a patient suffering from a disease associated with aberrant DNA methylation, comprising: administering to the patient a pharmaceutical composition comprising a therapeutically-effective amount of the compound of formula (I) or (III) or its salts or prodrugs as defined above and a pharmaceutically-acceptable carrier.
  • the pharmaceutical composition is administered orally, parenterally, topically, intraperitoneally, intravenously, intraarterially, transdermal ⁇ , sublingually, intramuscularly, rectally, transbuccally, intranasally, liposomally, via inhalation, vaginally, intraoccularly, via local delivery, subcutaneously, intraadiposally, intraarticularly, or intrathecally.
  • the pharmaceutical composition is administered orally.
  • the method further involves administering to the patient a second therapeutic agent in combination with the pharmaceutical composition.
  • the second therapeutic agent is decitabine or azacitidine.
  • the second therapeutic agent is selected from the group consisting of histone deacylase inhibitors, antibiotic agents, alkylating agents, retinoids, hormonal agents, plant-derived agents, biologic agents, interleukins, interferons, cytokines, immuno-modulating agents, and monoclonal antibodies.
  • the histone deacylase inhibitor is selected from the group consisting of trichostatin A, suberoylanilide hydroxamic acid, oxamflatin, suberic bishydroxamic acid, m-carboxy-cinnamic acid bishydroxamic acid, pyroxamide, trapoxin A, apicidin, depsipeptide, N-(2-amimophenyl)-4-[N- (pyridin-3-ylmethoxycarbonyl)aminomethyl] benzamide, butyric acid, phenylbutyrate and arginine butyrate.
  • the disease associated with aberrant DNA methylation is selected from the group consisting of hematological disorders, benign tumor and cancer.
  • the hematological disorder is selected from the group consisting of acute myeloid leukemia, acute promyelocytic leukemia, acute lymphoblastic leukemia, chronic myelogenous leukemia, myelodysplastic syndromes, and sickle cell anemia.
  • the disease is cancer and is selected from group consisting of breast cancer, skin cancer, bone cancer, prostate cancer, liver cancer, lung cancer, non-small cell lung cancer, brain cancer, cancer of the larynx, gall bladder, pancreas, rectum, parathyroid, thyroid, adrenal, neural tissue, head and neck, colon, stomach, bronchi, and kidney cancer, basal cell carcinoma, squamous cell carcinoma of both ulcerating and papillary type, metastatic skin carcinoma, osteo sarcoma, Ewing's sarcoma, veticulum cell sarcoma, myeloma, giant cell tumor, small-cell lung tumor, gallstones, islet cell tumor, primary brain tumor, acute and chronic lymphocytic and granulocytic tumors, hairy-cell tumor, adenoma, hyperplasia, medullary carcinoma, pheochromocytoma, mucosal neuronms, intestinal ganglioneuromas, hyperplastic corneal nerve tumor, marfanoi
  • the present invention provides a method for inhibiting DNA methylation in a cell, comprising: contacting the cell with the compound of formula (I) or (III) or its salts or prodrugs as defined above, such that DNA methylation activity of the cell is inhibited, preferably by at least 25%, more preferably by at least 50%, relative to the DNA methylation activity prior to the administration of the compound.
  • the present invention provides a method for selectively inhibiting activity of DNA methyltransferase DNMT1 in a cell, comprising: contacting a cell with the compound of the present invention, such that activity of DNA methyltransferase DNMT1 in the cell is inhibited more than that of DNA methyltransferase DNMT3a or DNMT3b.
  • the activity of DNA methyltransferase DNMT1 is inhibited via degradation of DNA methyltransferase DNMT1.
  • the step of contacting includes contacting the cell with a biologically effective amount of the compound of present invention, such that at least 50% of the activity of DNA methyltransferase DNMT1 in the cell is inhibited.
  • the step of contacting includes contacting the cell with a biologically effective amount of the compound of the present invention, such that at least 25% of the activity of DNA methyltransferase DNMT1 in the cell is inhibited.
  • the present invention provides a method for restoring activity of a DNA methylation-suppressed gene in a cell, comprising: contacting a cell with a biologically effective amount of the compound of the present invention, such that activity of the DNA methylation-suppressed gene is elevated by at least 25%, preferably at least 50%, relative to that in the absence of the compound.
  • the activity of the DNA methylation-suppressed gene includes but is not limited to transcriptional activity of the methylation- suppressed gene.
  • the present invention provides a method for treating a patient suffering from a disease associated with aberrant DNA methylation, comprising: administering to the patient a pharmaceutical composition comprising a therapeutically-effective amount of the compound of formula (I) or (III) or its salts or prodrugs as defined above and a pharmaceutically-acceptable carrier.
  • the pharmaceutical composition is administered orally, parenterally, topically, intraperitoneal ⁇ , intravenously, intraarterially, transdermal ⁇ , sublingually, intramuscularly, rectally, transbuccally, intranasally, liposomally, via inhalation, vaginally, intraoccularly, via local delivery, subcutaneously, intraadiposally, intraarticular ⁇ , or intrathecally.
  • the method further comprises: administering to the patient a second therapeutic agent in combination with the pharmaceutical composition.
  • the second therapeutic agent may be decitabine or azacitidine.
  • the second therapeutic agent may be selected from the group consisting of histone deacylase inhibitor, antibiotic agents, alkylating agents, retinoids, hormonal agents, plant-derived agents, biologic agents, interleukins, interferons, cytokines, immuno-modulating agents, and monoclonal antibodies.
  • the disease associated with aberrant DNA methylation is selected from the group consisting of hematological disorders, benign tumor and cancer.
  • cancer examples include but are not limited to acute myeloid leukemia, acute promyelocytic leukemia, acute lymphoblastic leukemia, chronic myelogenous leukemia, myelodysplastic syndromes, and sickle cell anemia.
  • hematological disorder examples include but are not limited to breast cancer, skin cancer, bone cancer, prostate cancer, liver cancer, lung cancer, non-small cell lung cancer, brain cancer, cancer of the larynx, gall bladder, pancreas, rectum, parathyroid, thyroid, adrenal, neural tissue, head and neck, colon, stomach, bronchi, and kidney cancer, basal cell carcinoma, squamous cell carcinoma of both ulcerating and papillary type, metastatic skin carcinoma, osteo sarcoma, Ewing's sarcoma, veticulum cell sarcoma, myeloma, giant cell tumor, small-cell lung tumor, gallstones, islet cell tumor, primary brain tumor, acute and chronic lymphocytic and granulocytic tumors, hairy-cell tumor, adenoma, hyperplasia, medullary carcinoma, pheochromocytoma, mucosal neuronms, intestinal ganglioneuromas, hyperplastic corneal nerve tumor, marfanoid habitus
  • Figure 1 illustrates the increase of RNA expression levels of p16 by representative comounds of this invention at different concentrations.
  • the present invention provides compounds, compositions, formulations, kits, methods of use, and manufacture of quinoline derivatives, and more particularly to 4-anilinoquinoline derivatives as inhibitors of DNA methylation enzymes, modulators of DNA methylation and therapeutic agents for preventing or treating diseases associated with aberrant DNA methylation such as cancer and hematological malignancy.
  • the inventive 4-anilinoquinoline derivatives in comparison with 4-anilinoquinolinium bis- quaternary salts in the art, should be more specific in the inhibition of DNMT1 and/or in the inhibition of DNA methylation in the cell due to their fewer charged substitutes or the replacement of the quaternary quinolinium and/or the pyridinium functional groups with ones with lower pKa values.
  • the compounds of present invention should have reduced cytotoxicity and more specifically modulate DNA methylation activity in the cell.
  • compounds where Y is NHCO and Z is Q1 in Formula (I) can be prepared by reacting N-acetylaminobenzoic acids (9) with 4- nitroaniline using coupling reagents such as EDCI or CDI to give amides (10), which can be hydrolysed with dilute HCI in 1 ,4-dioxane to amines (11). These can be reacted with 4-pyridyl pyridiniumchloride to give amines (12). Quatemisation of these as above (for example, with MeOTs) gives pyridinium compounds (13), which can be reduced to amines (14) and then coupled with 4-chloroquinolines as before, and if necessary further processed, to give compounds of Formula (I).
  • R represents R 6 -R 9
  • the quinoline derivatives of the present invention encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other compound which, upon administration to an animal including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to prodrugs and pharmaceutically acceptable salts of the compounds of the invention, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents.
  • prodrug indicates a therapeutic agent that is prepared in an inactive form that is converted to an active form (i.e., drug) within the body or cells thereof by the action of endogenous enzymes or other chemicals and/or conditions.
  • prodrug versions of the quinoline derivatives of the invention may be prepared by forming one or more ester bond with any of the hydroxyl groups in the compounds using an organic compound containing a carboxyl group, or as SATE [(S-acetyl-2-thioethyl) phosphate) derivatives according to the methods disclosed in WO 93/2451 , or in WO 94/26764 and U.S. Patent No. 5,770,713.
  • pharmaceutically acceptable salts refers to physiologically and pharmaceutically acceptable salts of the compounds of the invention: i.e., salts that retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto.
  • 4- anilinoquinolinium bisquaternary salts are preferably excluded.
  • Pharmaceutically acceptable base addition salts are formed with metals or amines, such as alkali and alkaline earth metals or organic amines.
  • metals used as cations are sodium, potassium, magnesium, calcium, and the like.
  • suitable amines are N 1 N'- dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, dicyclohexylamine, ethylenediamine, N-methylglucamine, and procaine (see, for example, Berge et al., "Pharmaceutical Salts," J. of Pharma Sci., 1977, 66, 1-19).
  • the base addition salts of said acidic compounds are prepared by contacting the free acid form with a sufficient amount of the desired base to produce the salt in the conventional manner.
  • the free acid form may be regenerated by contacting the salt form with an acid and isolating the free acid in the conventional manner.
  • the free acid forms differ from their respective salt forms somewhat in certain physical properties such as solubility in polar solvents, but otherwise the salts are equivalent to their respective free acid for purposes of the present invention.
  • a "pharmaceutical addition salt” includes a pharmaceutically acceptable salt of an acid form of one of the components of the compositions of the invention. These include organic or inorganic acid salts of the amines. Suitable pharmaceutically acceptable salts are well known to those skilled in the art and include basic salts of a variety of inorganic and organic acids, such as, for example, with inorganic acids, for example hydrochloric acid, hydrobromic acid, sulfuric acid or phosphoric acid; with organic carboxylic, sulfonic, sulfo or phospho acids or N-substituted sulfamic acids, for example acetic acid, propionic acid, glycolic acid, succinic acid, maleic acid, hydroxymaleic acid, methylmaleic acid, fumaric acid, malic acid, tartaric acid, lactic acid, oxalic acid, gluconic acid, glucaric acid, glucuronic acid, citric acid, benzoic acid, cinnamic acid
  • Pharmaceutically acceptable salts of compounds may also be prepared with a pharmaceutically acceptable cation.
  • Suitable pharmaceutically acceptable cations are well known to those skilled in the art and include alkaline, alkaline earth, ammonium and quaternary ammonium cations. Carbonates or hydrogen carbonates are also possible.
  • the invention also embraces isolated compounds.
  • An isolated compound refers to a compound which represents at least 10%, preferably 20%, more preferably 50% and most preferably 80% of the compound present in the mixture, and exhibits a detectable (i.e., statistically significant) inhibitory activity of DNA methylation directly or indirectly when tested in biological assays such as the combined bisulfite restriction analysis or COBRA (Xiong, Z.; Laird, P. W. Nucleic Acids Res. 1997, 25, 2532-2534), radiolabeled methyl incorporation assay (Francis, K. T.; Thompson, R. W.; Krumdieck, C. L. Am. J. CHn. Nutr.
  • the compounds of the present invention selectively inhibit activity of DNMT1 relative to DNMT3a and DNMT3b.
  • the compounds of the present invention can be formulated into pharmaceutically acceptable compositions for treating various diseases and conditions.
  • compositions of the present invention comprise one or more compounds of the invention in association with one or more nontoxic, pharmaceutically-acceptable carriers and/or diluents and/or adjuvants and/or excipients, collectively referred to herein as "carrier" materials, and if desired other active ingredients.
  • the compounds of the present invention are administered by any route, preferably in the form of a pharmaceutical composition adapted to such a route, as illustrated below and are dependent on the condition being treated.
  • the compounds and compositions can be, for example, administered orally, parenterally, intraperitoneally, intravenously, intraarterially, transdermally, sublingually, intramuscularly, rectally, transbuccally, intranasally, liposomally, via inhalation, vaginally, intraoccularly, via local delivery (for example by a catheter or stent), subcutaneously, intraadiposally, intraarticular ⁇ , or intrathecally.
  • the pharmaceutical formulation may optionally further include an excipient added in an amount sufficient to enhance the stability of the composition, maintain the product in solution, or prevent side effects (e.g., potential ulceration, vascular irritation or extravasation) associated with the administration of the inventive formulation.
  • excipients include, but are not limited to, mannitol, sorbitol, lactose, dextrose, cyclodextrin such as, ⁇ -, ⁇ -, and ⁇ -cyclodextrin, and modified, amorphous cyclodextrin such as hydroxypropyl-, hydroxyethyl-, glucosyl-, maltosyl-, maltotriosyl-, carboxyamidomethyl-, carboxymethyl-, sulfobutylether-, and diethylamino- substituted ⁇ , ⁇ -, and ⁇ -cyclodextrin.
  • Cyclodextrins such as Encapsin® from Janssen Pharmaceuticals or
  • the pharmaceutical compositions can be in the form of, for example, a tablet, capsule, suspension or liquid.
  • the pharmaceutical composition is preferably made in the form of a dosage unit containing a therapeutically-effective amount of the active ingredient. Examples of such dosage units are tablets and capsules.
  • the tablets and capsules which can contain, in addition to the active ingredient, conventional carriers such as binding agents, for example, acacia gum, gelatin, polyvinylpyrrolidone, sorbitol, or tragacanth; fillers, for example, calcium phosphate, glycine, lactose, maize-starch, sorbitol, or sucrose; lubricants, for example, magnesium stearate, polyethylene glycol, silica, or talc; disintegrants, for example, potato starch, flavoring or coloring agents, or acceptable wetting agents.
  • binding agents for example, acacia gum, gelatin, polyvinylpyrrolidone, sorbitol, or tragacanth
  • fillers for example, calcium phosphate, glycine, lactose, maize-starch, sorbitol, or sucrose
  • lubricants for example, magnesium stearate, polyethylene glycol, silica, or talc
  • disintegrants
  • Oral liquid preparations generally are in the form of aqueous or oily solutions, suspensions, emulsions, syrups or elixirs may contain conventional additives such as suspending agents, emulsifying agents, non-aqueous agents, preservatives, coloring agents and flavoring agents.
  • additives for liquid preparations include acacia, almond oil, ethyl alcohol, fractionated coconut oil, gelatin, glucose syrup, glycerin, hydrogenated edible fats, lecithin, methyl cellulose, methyl or propyl para-hydroxybenzoate, propylene glycol, sorbitol, or sorbic acid.
  • the compounds of the present invention can also be prepared in suitable forms to be applied to the skin, or mucus membranes of the nose and throat, and can take the form of creams, ointments, liquid sprays or inhalants, lozenges, or throat paints.
  • suitable forms can include chemical compounds such as dimethylsulfoxide (DMSO) to facilitate surface penetration of the active ingredient.
  • DMSO dimethylsulfoxide
  • the compounds of the present invention can be presented in liquid or semi-liquid form formulated in hydrophobic or hydrophilic bases as ointments, creams, lotions, paints or powders.
  • the compounds of the present invention can be administered in the form of suppositories admixed with conventional carriers such as cocoa butter, wax or other glyceride.
  • the compounds of the present invention can be in powder form for reconstitution in the appropriate pharmaceutically acceptable carrier at the time of delivery.
  • compositions can be administered via injection.
  • Formulations for parenteral administration can be in the form of aqueous or non-aqueous isotonic sterile injection solutions or suspensions. These solutions or suspensions can be prepared from sterile powders or granules having one or more of the carriers mentioned for use in the formulations for oral administration.
  • the compounds can be dissolved in polyethylene glycol, propylene glycol, ethanol, corn oil, benzyl alcohol, sodium chloride, and/or various buffers.
  • the compounds or formulations of the present invention can be administered by any route, preferably in the form of a pharmaceutical composition adapted to such a route, as illustrated below and are dependent on the condition being treated.
  • the compounds or formulations can be, for example, administered orally, parenterally, topically, intraperitoneally, intravenously, intraarterially, transdermal ⁇ , sublingually, intramuscularly, rectally, transbuccally, intranasally, liposomally, via inhalation, vaginally, intraoccularly, via local delivery (for example by catheter or stent), subcutaneously, intraadiposally, intraarticularly, or intrathecally.
  • the compounds and/or compositions according to the invention may also be administered or co-administered in slow release dosage forms.
  • compositions of this invention may be administered or co-administered in any conventional dosage form.
  • Co- administration in the context of this invention is defined to mean the administration of more than one therapeutic agent in the course of a coordinated treatment to achieve an improved clinical outcome.
  • Such coadministration may also be coextensive, that is, occurring during overlapping periods of time.
  • inventive compound or the composition containing the inventive compound may be administered into a host such as a patient at a dose of 0.1-1000 mg/ m 2 , optionally 1-200 mg/m 2 , optionally 1-50 mg/m 2 , optionally 1-40 mg/m 2 , optionally 1-30 mg/m 2 , optionally 1-20 mg/m 2 , or optionally 5-30 mg/m 2 .
  • the pharmaceutical formulations may be co-administered in any conventional form with one or more member selected from the group comprising infusion fluids, therapeutic compounds, nutritious fluids, antimicrobial fluids, buffering and stabilizing agents.
  • Patients may receive the pharmaceutical formulations intravenously.
  • the preferred route of administration is by intravenous infusion.
  • the pharmaceutical formulations of the current invention may be infused directly, without prior reconstitution.
  • Patients may be infused with the pharmaceutical formulations for 1 , 2, 3, 4, 5 or more hours, as a result of the enhanced stability of the formulations. Prolonged periods of infusion enable flexible schedules of administration of therapeutic formulations.
  • speed and volume of the infusion can be regulated according to the patient's needs.
  • the regulation of the infusion of the pharmaceutical formulations can be performed according to existing protocols.
  • the pharmaceutical formulations may be co-infused in any conventional form with one or more member selected from the group comprising infusion fluids, therapeutic compounds, nutritious fluids, antimicrobial fluids, buffering and stabilizing agents.
  • therapeutic components including, but are not limited to, anti-neoplastic agents, alkylating agents, agents that are members of the retinoids superfamily, antibiotic agents, hormonal agents, plant-derived agents, biologic agents, interleukins, interferons, cytokines, immuno-modulating agents, and monoclonal antibodies, may be co-infused with the inventive formulations.
  • Co-infusion in the context of this invention is defined to mean the infusion of more than one therapeutic agent in a course of coordinated treatment to achieve an improved clinical outcome.
  • Such co-infusion may be simultaneous, overlapping, or sequential.
  • co- infusion of the pharmaceutical formulations and infusion fluids may be performed through Y-type connector.
  • the pharmacokinetics and metabolism of intravenously administered the pharmaceutical formulations resemble the pharmacokinetics and metabolism of intravenously administered the inventive compound.
  • the compounds or pharmaceutical formulations of the present invention may be used in conjunction with a cytidine analog, such as 5-aza-2'- deoxycytidine (decitabine), and 5-aza-cytidine (azacitidine).
  • a cytidine analog such as 5-aza-2'- deoxycytidine (decitabine), and 5-aza-cytidine (azacitidine).
  • Decitabine is an antagonist of its related natural nucleoside, deoxycytidine.
  • the only structural difference between these two compounds is the presence of a nitrogen at position 5 of the cytosine ring in decitabine as compared to a carbon at this position for deoxycytidine.
  • Decitabine possesses multiple pharmacological characteristics. At a molecular level, it is S-phase dependent for incorporation into DNA. At a cellular level, decitabine can induce cell differentiation and exert hematological toxicity.
  • decitabine The most prominent function of decitabine is its ability to specifically and potently inhibit DNA methylation. As described above for methylation of cytosine in CpG islands as an example, methylation of cytosine to 5-methylcytosine occurs at the level of DNA. Inside the cell, decitabine is first converted into its active form, the phosphorylated 5-aza-deoxycytidine, by deoxycytidine kinase which is primarily synthesized during the S phase of the cell cycle. The affinity of decitabine for the catalytical site of deoxycytidine kinase is similar to the natural substrate, deoxycytidine.
  • decitabine After conversion to its triphosphate form by deoxycytidine kinase, decitabine is incorporated into replicating DNA at a rate similar to that of the natural substrate, dCTP. Bouchard and Momparler (1983) MoI. Pharmacol. 24:109-114.
  • the compounds or pharmaceutical formulations of the present invention may be used in conjunction with inhibitors of histone deacetylase (HDAC) to further modulate transcription of genes, e.g., to reestablish transcription of genes silenced by hypermethylation and acetylation of histones, in a synergistic manner.
  • HDAC histone deacetylase
  • the compounds or pharmaceutical formulations of the present invention may be used in conjunction with inhibitors of histone deacetylase (HDAC) to further modulate transcription of genes, e.g., to reestablish transcription of genes silenced by hypermethylation and acetylation of histones, in a synergistic manner.
  • HDAC histone deacetylase
  • HDAC histone acetyl transferase
  • HDACs histone deacetylases
  • HDACs With the removal of the acetyl groups from the histone lysine by HDACs, a positive charge is restored to the lysine residue, thereby condensing the structure of nucleosome and silencing the genes contained within. Thus, to activate these genes silenced by deacetylase of histones, the activity of HDACs should be inhibited. With the inhibition of HDAC, histones are acetylated and the DNA that is tightly wrapped around a deacetylated histone core relaxes. The opening of DNA conformation leads to expression of specific genes.
  • HDACs may also regulated gene expression by deacetylating transcription factors, such as p53 (a tumor suppressor gene), GAT A-1 , TFIIE, and TFIIF. Gu and Roeder (1997) Ce// 90:595-606 (p53); and Boyes et al. (1998) Nature 396:594-598 (GATA-1 ). HDACs also participate in cell cycle regulation, for example, by transcription repression which is mediated by RB tumor suppressor proteins recruiting HDACs. Brehm et al. (1998) Nature 391 :597-601. Thus, inhibition of HDACs should activate expression of tumor suppressor genes such as p53 and RB and as a result promote cell growth arrest, differentiation and apoptosis induced by these genes.
  • aberrant transcriptional silencing of a number of genes is directly related to pathogenesis of cancer and other diseases.
  • Methylation of cytosine residues in DNA and removal of acetyl groups from histones are the two primary mechanisms for gene silencing. Due to methylation and/or histone deacetylase of cancer-related genes, expression of these genes is suppressed or completely silenced. Meanwhile, expression of these genes is required for induction of growth arrest, differentiation, and/or apoptotic cell death of transformed cells. Inaction of these genes in the transformed cells leads to uncontrolled proliferation of these cells, which eventually results in cancer.
  • inventive compounds/compositions By combining the inventive compounds/compositions with HDAC inhibitors, genes required for induction of growth arrest, differentiation and cell death of transformed cells can be reactivated effectively.
  • the inventive compounds/compositions inhibit methylation of DNA for the genes, especially in the regulatory region, thus resulting in activation of transcription of the gene.
  • HDAC inhibitors inhibit deacetylase of the histones in the nucleosomal core of the gene, thus resulting in net increase of the acetylation of histones, which, in turn, activates transcription of the gene.
  • the combination therapy may reestablish gene transcription more effectively and, ideally, in a synergistic manner.
  • a combination therapy having synergistic effects should require a less amount of each inhibitor than it being used alone, thus reducing potential side effects associated systemic administration of high dosages of the inhibitors and improving therapeutic index.
  • anticancer agents exert their anti-cancer effects by triggering signal transduction cascades involving proteins encoded by these tumor suppressor genes. With insufficient expression of these genes in cancer cells, the anti-cancer effects of these anti-neoplastic agents may be severely reduced or completely eradicated.
  • the intrinsic defense mechanisms of the body are mobilized to combat the disease by restoration of the tumor-suppressing functions to cancer cells in response to signals sent by the anti-cancer agent administered. Such stimulation of the intrinsic tumor suppressing functions of the body should lead to the requirement of lower dosage of the anticancer agent, thus resulting in a higher therapeutic index (i.e., greater efficacy and lower toxicity) of the agent.
  • Inhibitors of HDACs include, but are not limited to, the following structural classes: 1) hydroxamic acids, 2) cyclic peptides, 3) benzamides, and 4) short-chain fatty acids.
  • hydroxamic acids and hydroxamic acid derivatives include trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA), oxamflatin, suberic bishydroxamic acid (SBHA), m-carboxy-cinnamic acid bishydroxamic acid (CBHA), and pyroxamide.
  • TSA was isolated as an antifungal antibiotic (Tsuji et al (1976) J.
  • HDAC-resistant cell lines have an altered HDAC evidences that this enzyme is an important target for TSA.
  • Other hydroxamic acid-based HDAC inhibitors, SAHA, SBHA, and CBHA are synthetic compounds that are able to inhibit HDAC at micromolar concentration or lower in vitro or in vivo. Glick et al. (1999) Cancer Res. 59:4392-4399.
  • hydroxamic acid-based HDAC inhibitors all possess an essential structural feature: a polar hydroxamic terminal linked through a hydrophobic methylene spacer (e.g., 6 carbon at length) to another polar site which is attached to a terminal hydrophobic moiety (e.g., benzene ring).
  • a polar hydroxamic terminal linked through a hydrophobic methylene spacer (e.g., 6 carbon at length) to another polar site which is attached to a terminal hydrophobic moiety (e.g., benzene ring).
  • a hydroxamic acid-based HDAC inhibitors all possess an essential structural feature: a polar hydroxamic terminal linked through a hydrophobic methylene spacer (e.g., 6 carbon at length) to another polar site which is attached to a terminal hydrophobic moiety (e.g., benzene ring).
  • a terminal hydrophobic moiety e.g., benzene ring
  • Cyclic peptides used as HDAC inhibitors are mainly cyclic tetra peptides.
  • cyclic peptides include, but are not limited to, trapoxin A, apicidin and FR901228.
  • Trapoxin A is a cyclic tetrapeptide that contains a 2-amino-8-oxo-9,10-epoxy-decanoyl (AOE) moiety.
  • AOE 2-amino-8-oxo-9,10-epoxy-decanoyl
  • FR901228 is a depsipeptide that is isolated from Chromobacterium violaceum, and has been shown to inhibit HDAC activity at micromolar concentrations.
  • Examples of benzamides include but are not limited to MS-27- 275. Saito et al. (1990) Proc. Natl. Acad. Sci. USA. 96:4592-4597.
  • Examples of short-chain fatty acids include but are not limited to butyrates (e.g., butyric acid, arginine butyrate and phenylbutyrate (PB)).
  • PB phenylbutyrate
  • depudecin which has been shown to inhibit HDAC at micromolar concentrations (Kwon et al. (1998) Proc. Natl. Acad. Sci. USA. 95:3356-3361 ) also falls within the scope of histone deacetylase inhibitor of the present invention.
  • the compounds or pharmaceutical formulations of the present invention may also be used in conjunction with other therapeutic components including but not limiting to anti-neoplastic agents, alkylating agents, agents that are members of the retinoids superfamily, antibiotic agents, hormonal agents, plant-derived agents, biologic agents, interleukins, interferons, cytokines, immuno-modulating agents, and monoclonal antibodies.
  • other therapeutic components including but not limiting to anti-neoplastic agents, alkylating agents, agents that are members of the retinoids superfamily, antibiotic agents, hormonal agents, plant-derived agents, biologic agents, interleukins, interferons, cytokines, immuno-modulating agents, and monoclonal antibodies.
  • an alkylating agent is used in combination with and/or added to the inventive compound/formulation.
  • alkylating agents include, but are not limited to bischloroethylamines (nitrogen mustards, e.g., chlorambucil, cyclophosphamide, ifosfamide, mechlorethamine, melphalan, uracil mustard), aziridines (e.g., thiotepa), alkyl alkone sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomustine, streptozocin), nonclassic alkylating agents (altretamine, dacarbazine, and procarbazine), platinum compounds (carboplastin and cisplatin).
  • nitrogen mustards e.g., chlorambucil, cyclophosphamide, ifosfamide, mechlorethamine, melphalan,
  • cisplatin, carboplatin or cyclophosphamide is used in combination with and/or added to the inventive compound/formulation.
  • a member of the retinoids superfamily is used in combination with and/or added to the inventive compound/formulation.
  • Retinoids are a family of structurally and functionally related molecules that are derived or related to vitamin A (all-trans-retinol). Examples of retinoid include, but are not limited to, all-trans-retinol, all-trans-retinoic acid (tretinoin), 13-cis retinoic acid (isotretinoin) and 9-cis-retinoic acid.
  • a hormonal agent is used in combination with and/or added to the inventive compound/formulation.
  • a hormonal agent are synthetic estrogens (e.g., diethylstibestrol), antiestrogens (e.g., tamoxifen, toremifene, fluoxymesterol and raloxifene), antiandrogens (bicalutamide, nilutamide, flutamide), aromatase inhibitors (e.g., aminoglutethimide, anastrozole and tetrazole), ketoconazole, goserelin acetate, leuprolide, megestrol acetate and mifepristone.
  • synthetic estrogens e.g., diethylstibestrol
  • antiestrogens e.g., tamoxifen, toremifene, fluoxymesterol and raloxifene
  • antiandrogens bicalutamide, nilutamide, flutamide
  • a plant-derived agent is used in combination with and/or added to the inventive compound/formulation.
  • plant-derived agents include, but are not limited to, vinca alkaloids (e.g., vincristine, vinblastine, vindesine, vinzolidine and vinorelbine), camptothecin (20(S)-camptothecin, 9-nitro-20(S)-camptothecin, and 9-amino- 20(S)-camptothecin), podophyllotoxins (e.g., etoposide (VP-16) and teniposide (VM-26)), and taxanes (e.g., paclitaxel and docetaxel).
  • vinca alkaloids e.g., vincristine, vinblastine, vindesine, vinzolidine and vinorelbine
  • camptothecin (20(S)-camptothecin, 9-nitro-20(S)-camptothecin, and 9-amino- 20(S)-campto
  • a biologic agent is used in combination with and/or added to the inventive compound/formulation, such as immuno- modulating proteins such as cytokines, monoclonal antibodies against tumor antigens, tumor suppressor genes, and cancer vaccines.
  • interleukins examples include, but are not limited to, interleukin 2 (IL-2), and interleukin 4 (IL-4), interleukin 12 (IL-12).
  • interferons examples include, but are not limited to, interferon ⁇ , interferon ⁇ (fibroblast interferon) and interferon Y (fibroblast interferon).
  • cytokines examples include, but are not limited to erythropoietin (epoietin), granulocyte-CSF (filgrastim), and granulocyte, macrophage-CSF (sargramostim).
  • Immuno- modulating agents other than cytokines include, but are not limited to bacillus Calmette-Guerin, levamisole, and octreotide.
  • Example of monoclonal antibodies against tumor antigens that can be used in conjunction with the inventive formulations include, but are not limited to, HERCEPTIN® (Trastruzumab), RITUXAN® (Rituximab), MYLOTARG® (anti-CD33 antibody), and CAMPATH® (anti-CD52 antibody).
  • a kinase inhibitor is used in combination with and/or added to the inventive compound/formulation for treating diseases associated with abnormal kinase activity.
  • the tyrosine kinase inhibitor is imatanib mesylate (e.g., Gleevec®).
  • Imatanib mesylate is a protein tyrosine kinase inhibitor that inhibits the Bcr-Abl tyrosine kinase created by the Philadelphia chromosome abnormality in CML. Imatanib mesylate achieves this inhibitory result through binding to the adenosine triphosphate-binding site of the Bcr-Abl tyrosine kinase, which prevents phosphorylation of substrates and related malignant transformation. Through inhibition of this kinase, it is believed that imatinib mesylate inhibits cell proliferation and induces apoptosis. T. Schindler et al (2000) Science 289:1938-1942.
  • the kinase is a serine/threonine kinase such as a Raf kinase; and the kinase inhibitor is BAY 43-9006.
  • the kinase is a protein kinase such as a Raf-mitogen-activated protein kinase (MEK) and protein kinase B (Akt) kinase.
  • MEK Raf-mitogen-activated protein kinase
  • Akt protein kinase B
  • the kinase is an extracellular signal- regulated kinase (ERK).
  • ERK extracellular signal- regulated kinase
  • Examples of the inhibitor of ERK include but are not limited to PD98059, PD184352, and U0126.
  • the kinase is a phosphatidylinositol 3 1 - kinase (PI3K).
  • PI3K phosphatidylinositol 3 1 - kinase
  • Examples of the inhibitor of PI3K include but are not limited to LY294002.
  • the kinase is a tyrosine kinase.
  • the tyrosine kinase may be a receptor tyrosine kinase and non-receptor tyrosine kinase.
  • Examples of the receptor tyrosine kinase include, but are not limited to, epidermal growth factor receptor family (EGFR), platelet-derived growth factor receptor (PDGFR) family, vascular endothelial growth factor receptor (VEGFR) family, nerve growth factor receptor (NGFR) family, fibroblast growth factor receptor family (FGFR) insulin receptor family, ephrin receptor family, Met family, and Ror family.
  • Examples of the epidermal growth factor receptor family include, but are not limited to, HER1 , HER2/neu, HER3, and HER4.
  • inhibitors of epidermal growth factor receptor family include, but are not limited to, HERCEPTIN®, ZD1839 (IRESSA®), PD168393, CI1033, IMC-C225, EKB-569, and inhibitors binding covalently to Cys residues of the receptor tyrosine kinase.
  • diseases associated with abnormal activity of the epidermal growth factor receptor family include, but are not limited to, epithelial tumor, carcinoma, carcinoma of upper aerodigestive tract, lung cancer, and non-small cell lung cancer.
  • vascular endothelial growth factor receptor family examples include, but are not limited to, VEGFR1 , VEGFR2, and VEGFR3.
  • An example of the inhibitor of the vascular endothelial growth factor receptor family includes, but is not limited to, SU6668.
  • Examples of the disease associated with abnormal activity of the vascular endothelial growth factor receptor family include, but are not limited to, solid and metastasis-prone tumors.
  • nerve growth factor receptor family examples include, but are not limited to, trk, trkB and trkC.
  • Examples of the inhibitors of the nerve growth factor receptor family include, but are not limited to, CEP-701 , CEP-751 , and indocarbazole compound.
  • Examples of the diseases associated with abnormal activity of the nerve growth factor receptor family include, but are not limited to, prostate, colon, papillary and thyroid cancers, neuromas and osteoblastomas.
  • Met family examples include, but are not limited to, Met, TPR-Met, Ron, c-Sea, and v-Sea.
  • Examples of disease associated with activity of the receptor tyrosine kinase from Met family include, but are not limited to, invasively ingrowing tumor, carcinoma, papillary carcinoma of thyroid gland, colon, carcinoma, renal carcinoma, pancreatic carcinoma, ovarian carcinoma, head and neck squamous carcinoma.
  • non-receptor tyrosine kinase examples include, but are not limited to, c-kit family, Src family, Fes family, JAK family, Fak family, Btk family, Syk/ZAP-70 family, and AbI family.
  • non-receptor tyrosine kinases from the Src family include, but are not limited to, Src, c-Src, v-Src, Yes, c-Yes, v-Yes, Fyn, Lyn, Lck, BIk, Hck, Fgr, c-Fgr, v-Fgr, p561ck, Tk1 , Csk, and Ctk.
  • inhibitors of the non-receptor tyrosine kinase from the Src family include, but are not limited to, SU 101 and CGP 57418B.
  • Examples of the diseases associated with activity of the nonreceptor tyrosine kinase from the Src family include, but are not limited to, breast cancer, carcinoma, myeloma, leukemia, and neuroblastoma.
  • non-receptor tyrosine kinases from the Fes family include, but are not limited to, c-fes/fps, v-fps/fes, p94-c-fes-related protein, and Fer.
  • Examples of the diseases associated with activity of the nonreceptor tyrosine kinase from the Fes family include, but are not limited to, tumor of mesenchymal origin and tumor of hematopoietic origin.
  • non-receptor tyrosine kinases from the JAK family include, but are not limited to, Jak1 , Jak2, Tyk2, and Jak3.
  • Examples of the inhibitors of the non-receptor tyrosine kinase from the JAK family include, but are not limited to, tyrphostin, member of CIS/SOCS/Jab family, synthetic component AG490, dimethoxyquinazoline compound, 4-(phenyl)-amino-6,7-dimethoxyquinazoline, 4-(4'-hydroxyphenyl)- amino-6,7-dimethoxyquinazoline, 4-(3'-bromo-4'-hydroxylphenyl)-amino-6,7- dimethoxyquinazoline, and 4-(3',5'-dibromo-4'-hydroxylphenyl)-amino-6,7- dimethoxyquinazoline.
  • Examples of the diseases associated with activity of the nonreceptor tyrosine kinase from JAK family include, but are not limited to, tumor of mesenchymal origin and tumor of hematopoietic origin.
  • Examples of the non-receptor tyrosine kinases from the Fak family include, but are not limited to, Fak and CAK. beta. /Pyk2/RAFTK.
  • Examples of the inhibitors of the non-receptor tyrosine kinases from the Fak family include, but are not limited to, a dominant negative mutant S1034-FRNK; a metabolite FTY720 from lsaria sinclarii, and FAK antisense oligonucleotide ISIS 15421.
  • Examples of the diseases associated with abnormal activity of the non-receptor tyrosine kinases from Fak family include, but are not limited to, human carcinoma, metastasis-prone tumor, and tumor of hematopoietic origin.
  • non-receptor tyrosine kinase from the Btk family include, but are not limited to, Btk/Atk, Itk/Emt/Tsk, Bmx/Etk, and Itk, Tec, Bmx, and RIk.
  • inhibitors of the non-receptor tyrosine kinases from Btk family include, but are not limited to, alpha-cyano-beta-hydroxy-beta- met-hyl-N-(2,5-dibromophenyl)propenamide.
  • diseases associated with abnormal activity of the non-receptor tyrosine kinase from the Btk family include, but are not limited to, B-lineage leukemia and lymphoma.
  • non-receptor tyrosine kinases from the Syk/ZAP- 70 family include, but are not limited to, Syk and ZAP-70.
  • inhibitors of the non-receptor tyrosine kinases from the Syk/ZAP-70 family include, but are not limited to, piceatannol, 3,4- dimethyl-10-(3-aminopropyl)-9-acridone oxalate, acridone-related compound, Lys-Leu-lle-Leu-Phe-Leu-Leu-Leu [SEQ ID NO: 1 ) peptide, and peptide containing Lys-Leu-lle-Leu-Phe-Leu-Leu-Leu motif.
  • Examples of the diseases associated with abnormal activity of the non-receptor tyrosine kinases from the Syk/ZAP-70 family include, but are not limited to, benign breast cancer, breast cancer, and tumor of mesenchymal origin. 5. Indications for Compounds or Pharmaceutical Compositions of the Present Invention
  • the pharmaceutical formulations according to the present invention may be used to treat a wide variety of diseases, preferably those associated with aberrant DNA methylation.
  • Preferable indications that may be treated using the pharmaceutical formulations of the present invention include those often involving undesirable or uncontrolled cell proliferation.
  • Such indications include benign tumors, various types of cancers such as primary tumors and tumor metastasis, restenosis (e.g., coronary, carotid, and cerebral lesions), hematological disorders, abnormal stimulation of endothelial cells (atherosclerosis), insults to body tissue due to surgery, abnormal wound healing, abnormal angiogenesis, diseases that produce fibrosis of tissue, repetitive motion disorders, disorders of tissues that are not highly vascularized, and proliferative responses associated with organ transplants.
  • benign tumors include benign tumors, various types of cancers such as primary tumors and tumor metastasis, restenosis (e.g., coronary, carotid, and cerebral lesions), hematological disorders, abnormal stimulation of endothelial cells (atherosclerosis), insults to body tissue due to surgery, abnormal wound healing, abnormal angiogenesis, diseases that produce fibrosis of tissue, repetitive
  • a benign tumor is usually localized and nonmetastatic.
  • Specific types benign tumors that can be treated using the present invention include hemangiomas, hepatocellular adenoma, cavernous haemangioma, focal nodular hyperplasia, acoustic neuromas, neurofibroma, bile duct adenoma, bile duct cystanoma, fibroma, lipomas, leiomyomas, mesotheliomas, teratomas, myxomas, nodular regenerative hyperplasia, trachomas and pyogenic granulomas.
  • malignant tumors In a malignant tumor cells become undifferentiated, do not respond to the body's growth control signals, and multiply in an uncontrolled manner.
  • the malignant tumor is invasive and capable of spreading to distant sites (metastasizing).
  • Malignant tumors are generally divided into two categories: primary and secondary. Primary tumors arise directly from the tissue in which they are found.
  • a secondary tumor, or metastasis is a tumor which is originated elsewhere in the body but has now spread to a distant organ.
  • the common routes for metastasis are direct growth into adjacent structures, spread through the vascular or lymphatic systems, and tracking along tissue planes and body spaces (peritoneal fluid, cerebrospinal fluid, etc.)
  • cancer or malignant tumors include breast cancer, skin cancer, bone cancer, prostate cancer, liver cancer, lung cancer, brain cancer, cancer of the larynx, gall bladder, pancreas, rectum, parathyroid, thyroid, adrenal, neural tissue, head and neck, colon, stomach, bronchi, kidneys, basal cell carcinoma, squamous cell carcinoma of both ulcerating and papillary type, metastatic skin carcinoma, osteo sarcoma, Ewing's sarcoma, veticulum cell sarcoma, myeloma, giant cell tumor, small-cell lung tumor, gallstones, islet cell tumor, primary brain tumor, acute and chronic lymphocytic and granulocytic tumors, hairy-cell tumor, adenoma, hyperplasia, medullary carcinoma, pheochromocytoma, mucosal neuronms, intestinal ganglioneuromas, hyperplastic corneal nerve tumor, marfanoid habit
  • Hematologic disorders include abnormal growth of blood cells which can lead to dysplastic changes in blood cells and hematologic malignancies such as various leukemias.
  • hematologic disorders include but are not limited to acute myeloid leukemia, acute promyelocytic leukemia, acute lymphoblastic leukemia, chronic myelogenous leukemia, the myelodysplastic syndromes, and sickle cell anemia.
  • AML Acute myeloid leukemia
  • Several inherited genetic disorders and immunodeficiency states are associated with an increased risk of AML. These include disorders with defects in DNA stability, leading to random chromosomal breakage, such as Bloom's syndrome, Fanconi's anemia, Li-Fraumeni kindreds, ataxia-telangiectasia, and X-linked agammaglobulinemia.
  • Acute promyelocytic leukemia represents a distinct subgroup of AML. This subtype is characterized by promyelocytic blasts containing the 15;17 chromosomal translocation. This translocation leads to the generation of the fusion transcript comprised of the retinoic acid receptor and a sequence PML.
  • ALL Acute lymphoblastic leukemia
  • Chronic myelogenous leukemia is a clonal myeloproliferative disorder of a pluripotent stem cell.
  • CML is characterized by a specific chromosomal abnormality involving the translocation of chromosomes 9 and 22, creating the Philadelphia chromosome. Ionizing radiation is associated with the development of CML.
  • the myelodysplastic syndromes are heterogeneous clonal hematopoietic stem cell disorders grouped together because of the presence of dysplastic changes in one or more of the hematopoietic lineages including dysplastic changes in the myeloid, erythroid, and megakaryocyte series. These changes result in cytopenias in one or more of the three lineages.
  • Patients afflicted with MDS typically develop complications related to anemia, neutropenia (infections), or thrombocytopenia (bleeding). Generally, from about 10% to about 70% of patients with MDS develop acute leukemia.
  • Treatment of abnormal cell proliferation due to insults to body tissue during surgery may be possible for a variety of surgical procedures, including joint surgery, bowel surgery, and cheloid scarring.
  • Diseases that produce fibrotic tissue include emphysema.
  • Repetitive motion disorders that may be treated using the present invention include carpal tunnel syndrome.
  • An example of cell proliferative disorders that may be treated using the invention is a bone tumor.
  • the proliferative responses associated with organ transplantation that may be treated using this invention include those proliferative responses contributing to potential organ rejections or associated complications. Specifically, these proliferative responses may occur during transplantation of the heart, lung, liver, kidney, and other body organs or organ systems.
  • Abnormal angiogenesis that may also be treated using this invention include those abnormal angiogenesis accompanying rheumatoid arthritis, ischemic-reperfusion related brain edema and injury, cortical ischemia, ovarian hyperplasia and hypervascularity, (polycystic ovary syndrome), endometriosis, psoriasis, diabetic retinopaphy, and other ocular angiogenic diseases such as retinopathy of prematurity (retrolental fibroplastic), muscular degeneration, corneal graft rejection, neuroscular glaucoma and Oster Webber syndrome.
  • abnormal angiogenesis accompanying rheumatoid arthritis, ischemic-reperfusion related brain edema and injury, cortical ischemia, ovarian hyperplasia and hypervascularity, (polycystic ovary syndrome), endometriosis, psoriasis, diabetic retinopaphy, and other ocular
  • corneal angiogenesis involves three phases: a pre-vascular latent period, active neovascularization, and vascular maturation and regression.
  • angiogenic factors including elements of the inflammatory response, such as leukocytes, platelets, cytokines, and eicosanoids, or unidentified plasma constituents have yet to be revealed.
  • the pharmaceutical formulations of the present invention may be used for treating diseases associated with undesired or abnormal angiogenesis.
  • the method comprises administering to a patient suffering from undesired or abnormal angiogenesis the pharmaceutical formulations of the present invention alone, or in combination with antineoplastic agent whose activity as an anti-neoplastic agent in vivo is adversely affected by high levels of DNA methylation.
  • the particular dosage of these agents required to inhibit angiogenesis and/or angiogenic diseases may depend on the severity of the condition, the route of administration, and related factors that can be decided by the attending physician. Generally, accepted and effective daily doses are the amount sufficient to effectively inhibit angiogenesis and/or angiogenic diseases.
  • the pharmaceutical formulations of the present invention may be used to treat a variety of diseases associated with undesirable angiogenesis such as retinal/choroidal neuvascularization and corneal neovascularization.
  • diseases associated with undesirable angiogenesis such as retinal/choroidal neuvascularization and corneal neovascularization.
  • retinal/choroidal neuvascularization include, but are not limited to, Bests diseases, myopia, optic pits, Stargarts diseases, Pagets disease, vein occlusion, artery occlusion, sickle cell anemia, sarcoid, syphilis, pseudoxanthoma elasticum carotid abostructive diseases, chronic uveitis/vitritis, mycobacterial infections, Lyme's disease, systemic lupus erythematosis, retinopathy of prematurity, Eales disease, diabetic retinopathy, macular degeneration, Bechets diseases, infections causing a retinitis or chroiditis, presumed ocular histo
  • corneal neuvascularization examples include, but are not limited to, epidemic keratoconjunctivitis, Vitamin A deficiency, contact lens overwear, atopic keratitis, superior limbic keratitis, pterygium keratitis sicca, sjogrens, acne rosacea, phylectenulosis, diabetic retinopathy, retinopathy of prematurity, corneal graft rejection, Mooren ulcer, Terrien's marginal degeneration, marginal keratolysis, polyarteritis, Wegener sarcoidosis, Scleritis, periphigoid radial keratotomy, neovascular glaucoma and retrolental fibroplasia, syphilis, Mycobacteria infections, lipid degeneration, chemical burns, bacterial ulcers, fungal ulcers, Herpes simplex infections, Herpes zoster infections, protozoan infections and Kaposi sarcoma.
  • the pharmaceutical formulations of the present invention may be used for treating chronic inflammatory diseases associated with abnormal angiogenesis.
  • the method comprises administering to a patient suffering from a chronic inflammatory disease associated with abnormal angiogenesis the pharmaceutical formulations of the present invention alone, or in combination with an anti-neoplastic agent whose activity as an anti-neoplastic agent in vivo is adversely affected by high levels of DNA methylation.
  • the chronic inflammation depends on continuous formation of capillary sprouts to maintain an influx of inflammatory cells.
  • the influx and presence of the inflammatory cells produce granulomas and thus, maintains the chronic inflammatory state.
  • Inhibition of angiogenesis using the pharmaceutical formulations of the present invention may prevent the formation of the granulosmas, thereby alleviating the disease.
  • Examples of chronic inflammatory disease include, but are not limited to, inflammatory bowel diseases such as Crohn's disease and ulcerative colitis, psoriasis, sarcoidois, and rheumatoid arthritis.
  • Inflammatory bowel diseases such as Crohn's disease and ulcerative colitis are characterized by chronic inflammation and angiogenesis at various sites in the gastrointestinal tract.
  • Crohn's disease occurs as a chronic transmural inflammatory disease that most commonly affects the distal ileum and colon but may also occur in any part of the gastrointestinal tract from the mouth to the anus and perianal area.
  • Patients with Crohn's disease generally have chronic diarrhea associated with abdominal pain, fever, anorexia, weight loss and abdominal swelling.
  • Ulcerative colitis is also a chronic, nonspecific, inflammatory and ulcerative disease arising in the colonic mucosa and is characterized by the presence of bloody diarrhea.
  • inflammatory bowel diseases are generally caused by chronic granulomatous inflammation throughout the gastrointestinal tract, involving new capillary sprouts surrounded by a cylinder of inflammatory cells. Inhibition of angiogenesis by the pharmaceutical formulations of the present invention should inhibit the formation of the sprouts and prevent the formation of granulomas.
  • the inflammatory bowel diseases also exhibit extra intestinal manifestations, such as skin lesions. Such lesions are characterized by inflammation and angiogenesis and can occur at many sites other the gastrointestinal tract. Inhibition of angiogenesis by the pharmaceutical formulations of the present invention should reduce the influx of inflammatory cells and prevent the lesion formation.
  • Sarcoidois another chronic inflammatory disease, is characterized as a multi-system granulomatous disorder.
  • the granulomas of this disease can form anywhere in the body and, thus, the symptoms depend on the site of the granulomas and whether the disease is active.
  • the granulomas are created by the angiogenic capillary sprouts providing a constant supply of inflammatory cells.
  • Psoriasis also a chronic and recurrent inflammatory disease, is characterized by papules and plaques of various sizes. Treatment using the pharmaceutical formulations of the present invention should prevent the formation of new blood vessels necessary to maintain the characteristic lesions and provide the patient relief from the symptoms.
  • Rheumatoid arthritis is also a chronic inflammatory disease characterized by non-specific inflammation of the peripheral joints. It is believed that the blood vessels in the synovial lining of the joints undergo angiogenesis. In addition to forming new vascular networks, the endothelial cells release factors and reactive oxygen species that lead to pannus growth and cartilage destruction. The factors involved in angiogenesis may actively contribute to, and help maintain, the chronically inflamed state of rheumatoid arthritis. Treatment using the pharmaceutical formulations of the present invention alone or in conjunction with other anti-RA agents may prevent the formation of new blood vessels necessary to maintain the chronic inflammation and provide the RA patient relief from the symptoms.
  • the pharmaceutical formulations of the present invention may be used for treating diseases associated with abnormal hemoglobin synthesis.
  • the method comprises administering the pharmaceutical formulations of the present invention to a patient suffering from disease associated with abnormal hemoglobin synthesis.
  • Decitabine containing formulations stimulate fetal hemoglobin synthesis because the mechanism of incorporation into DNA is associated with DNA hypomethylation.
  • diseases associated with abnormal hemoglobin synthesis include, but are not limited to, sickle cell anemia and ⁇ -thalassemia.
  • the pharmaceutical formulations of the present invention may be used to control intracellular gene expression.
  • the method comprises administering the pharmaceutical formulations of the present invention to a patient suffering from disease associated with abnormal levels of gene expression.
  • DNA methylation is associated with the control of gene expression.
  • methylation in or near promoters inhibit transcription while demethylation restores expression. Examples of the possible applications of the described mechanisms include, but are not limited to, therapeutically modulated growth inhibition, induction of apoptosis, and cell differentiation.
  • Gene activation facilitated by the pharmaceutical formulations of the present invention may induce differentiation of cells for therapeutic purposes.
  • Cellular differentiation is induced through the mechanism of hypomethylation.
  • Examples of morphological and functional differentiation include, but are not limited to differentiation towards formation of muscle cells, myotubes, cells of erythroid and lymphoid lineages.
  • A4 N 1 -(4-Pyridinyl)-1,3-benzenediamine.
  • A7 4- ⁇ 3-[(4-Ammoniobenzoyl)amino]anilino ⁇ -1-methylpyridinium dichloride (A7).
  • A6 (1.57 g, 4.08 mmol) was dissolved in 5:1 H 2 O:EtOH (62 ml_), Fe dust was added(1.1 g), and the resulting suspension was refluxed with vigorous stirring for 5 h.
  • the hot reaction mixture was filtered through a pad of Celite, and the Celite pad was washed with hot EtOH.
  • the combined EtOH fractions were evaporated to dryness, and the residue extracted with warm water. This solution was evaporated to dryness, and the residue was dried by azeotroping with methanol (3 x 30 ml_).
  • N-4-Nitrophenyl)-4-pyridinamine (B3).
  • 4-Toluenesulfonic acid (53.80 g, 0.28 mol) was dissolved in benzene (200 mL), and the resulting solution refluxed under Dean-Stark conditions for approximately 96 h, until evolution of H 2 O ceased.
  • phenol (112.25 g, 1.19 mol)
  • the resulting mixture refluxed under Dean-Stark conditions for approximately 1 h, until evolution of H 2 O ceased.
  • Nitroaniline B3 (-55.00 g, -0.26 mol) was brought to reflux in 2:1 EtOH:H 2 O (500 ml_), and then Fe dust (56.96 g, 1.02 mmol) and glacial acetic acid (10 ml_) were added. The resulting mixture was refluxed for 30 min, and then cooled to room temperature. The reaction mixture was basified by addition of aqueous NH 3 , and filtered to remove solids.
  • Ci 3 H 11 N 3 O 3 (M +1 ) m/z 258.0879, found 258.0875; Anal. CaIc. for C 13 H 11 N 3 O 3 : C, 60.7; H, 4.3; N, 16.3; found C, 60.7; H, 4.4; N, 16.6%.
  • Para- toluenesulfonic acid (2 g, 10.49 mmol) was azeotroped with benzene (250 ml_) for 2 h.
  • the hot reaction mixture was filtered through a pad of Celite, and the top layer of the Celite pad was boiled with more EtOH and filtered (this procedure was repeated three times to ensure complete extraction of product from iron residues).
  • the combined EtOH extracts were evaporated to dryness, and the residue was extracted with hot water, and filtered through a pad of Celite.
  • the filtrate was concentrated to a smaller volume, and then stirred in pre-washed ion-exchange resin (55 g).
  • the resulting slurry was loaded onto a column packed with pre-washed ion- exchange resin and eluted with water. Fractions containing product were combined and evaporated to dryness, and the residue was azeotroped several times with EtOH.
  • the reaction mixture was then cooled to room temperature and diluted with brine. The resulting mixture was warmed to obtain a precipitate, which was filtered and then oven-dried at 110 0 C. The solid was then extracted into boiling ethanol (5 ⁇ 150 ml_), and the combined EtOH extracts were evaporated to dryness. The resulting residue was stirred in dilute aqueous NH 3 , and the resulting precipitate was filtered. Further product was obtained by neutralizing the filtrate with glacial AcOH, and filtering the resulting precipitate.
  • R 4 is H
  • A is NH
  • X is H
  • R 6 - R 9 are H.
  • G7, G8, D1 , and D2 are CH.
  • reaction mixture was stirred at 20 0 C for 2 h, by this time TLC (SiO 2 /8%MeOH/DCM/aq NH3)and mass spectrum showed completion of the reaction. Then the reaction mixture was acidified with c. HCI, stirred for 1 h. at 20 0 C. After this time the reaction mixture was carefully neutralize with aqueous NH 3 . The MeOH was evaporated under reduced pressure and the aqueous residue was the stirred with aqueous NH 3 .
  • 3-[(2-Amino-6-methyl-4-pyrimidinyl)amino]benzoic acid hydrochloride(A9) 3-Amino benzoic acid (A7) (1.02g, 7.42 mmol) and 2- amino-6-chloro-4-methylpyrimidine (A8) (1.08 g, 7.42mmol) was dissolved in 2- ethoxyethanol by heating, then a drop of c.HCI was added, refluxed for 1 h. and cool to 20 0 C. The resulting precipitate was filtered washed with more 2-ethoxy ethanol followed by EtOAc.
  • COMPOUNDS (CPD. GG2, CPD. GG3, CPD. GG4, CPD. GG5)
  • reaction mixture was refluxed for 2 days, diluted with EtOAc (150 mL), brought to boil and allowed it to cool to 20 0 C.
  • EtOAc 150 mL
  • the resulting precipitate was filtered, washed with more EtOAc and dried to give a yellow solid 161 mg, which was purified by prep.
  • Cpd. VV2 ⁇ /- ⁇ 4-[(6-Amino-4-quinolinyl)amino]phenyl ⁇ -4-[(2,6-diamino-4- pyrimidinyl)amino]benzamide dihydrochloride(Cpd. VV2).
  • Residue was redissolved in MeOH and evaporated to dryness, and then recrystallized from MeOH/EtOAc to give 178 mg of the product; this was only 93 % clean by HPLC. This was then converted to free base by stirring in aq NH 3 filtered, air dried and chromatographed on neutral alumina eluting with a gradient( 0-7.5%) of MeOH/DCM containing 1.5% aq NH 3 to give clean free base of Cpd. VV2. This was then converted to HCI salt by dissolving in MeOH and adding 1.25 M HCI in MeOH. Evaporated to dryness and the residue was recrystallized from MeOH/ EtOAc to give Cpd.
  • the resulting solid was re-dissolved in MeOH ( ⁇ 5 L), and this solution was filtered through Celite to remove undissolved impurities, and then concentrated to a smaller volume under reduced pressure. The resulting solid was collected by filtration, then re-suspended in and washed sequentially with EtOH, MeOH, and EtOAc, and finally collected again by filtration.
  • 4-(4-Aminophenylthio)pyridin-2-amine (9).
  • 4-aminobenzene thiol (1) (9.49 g, 75.77 mmol) in dry DMF (54 mL) were sequentially added 4-chloro-2-aminopyridine (8) (3.70 g, 28.80 mmol) and dry K 2 CO 3 (10.70 g, 107.97 mmol), and the resulting yellow suspension stirred at -120 0 C (bath temperature) for -45 min. After this time, the resultant brown- black suspension was cooled to room temperature, and then diluted with H 2 O and EtOAc.
  • the resulting material was re-dissolved in MeOH and adsorbed onto a quantity of silica gel, and the resulting silica adsorbate was purified by column chromatography on silica gel, eluting with 1% ⁇ 10% MeOH:CH 2 CI 2 (with 0.5% aq.NH 3 ), to afford cleaner material.
  • This material was purified further by re- precipitation from MeOH:methanolic HChEtOAc, to afford Cpd.
  • the demethylating activity of non-bis-quaternary 4- anilinoquinolines were tested in a cell-based GFP (green fluorescent protein) assay.
  • GFP green fluorescent protein
  • This assay has a GFP gene regulated by the CMV promoter and is sensitive to the methylation of CpG sites within the promoter. A decrease in methylation resulting from exposure to a methylation inhibitor leads to GFP expression and is readily scored.
  • the CMV-EE210 cell line containing the epigenetically silenced GFP transgene was used to assay for reactivation of GFP expression by flow cytometry.
  • CMV-EE210 was made by transfecting NIH 3T3 cells with the pTR-UF/UF1/UF2 plasmid (Zolotuhin et al., 1996), which is comprised of pBS(+) (Stratagene, Inc.) containing a cytomegalovirus (CMV) promoter driving a humanized GFP gene adapted for expression in mammalian cells.
  • CMV cytomegalovirus
  • high-level GFP expressing cells were initially selected by FACS analysis and sorting using a MoFIo cytometer (Cytomation, Inc.).
  • Decitabine potent inhibitor of mammalian DNMT1 , was used as a positive control.
  • decitabine at 1 ⁇ M or a test compound (at a concentration of 30-50 ⁇ M) was added to complete medium (phenol red free DMEM (Gibco, Life Technologies) supplemented with 10% fetal bovine serum (Hyclone)). Cells were then seeded to 30% confluence ( ⁇ 5000 cell/well) in 96 well plate containing the test compounds and grown for three days in at 37 0 C in 5% CO 2 . The plates were examined under a fluorescent microscope using a 450-490 excitation filter (I3 filter cube, Leica, Deerfield IL).
  • GFP IC 50 is the concentration of an inhibitor that (like an IC 50 ) is the dose at which the GFP expression level goes from g3 to g1/2.
  • Table 3 of the compounds tested, six compounds (Cpd. DDD5, Cpd. DDD6, Cpd. DDD7, Cpd. DDD8, Cpd. DDD9, and Cpd. DDD10) reactivated transcription of the GFP gene at greater than 75% level. In addition, they are less than one-half as toxic as decitabine.
  • RKO and HCT-116 cells were treated with SN31439.CI, SN31486.CI, and SN31575.CL at varying concentrations. After a forty eight hour incubation cells were harvested for RNA isolation using the Qiagen RNeasy Mini kit. RNA was quantified using a spectrophotometer and 1 ⁇ g of RNA was used for cDNA synthesis using the Bio-Rad iScript cDNA Synthesis Kit. RTPCR was performed using SYBER GreenER qPCR SuperMix for iCycler according to the manufacturer's protocol.
  • Primer sequences used are as follows p16 5'-atgtcctgccttttaacgta-3' and 5'-gtgctcactccagaaaactc-3', MLH-1 5'-tgaggaagggaacctgattg-3' and 5'- tcttcgtcccaattcacctc-3', p15 5'- caccatgaagcgaaacacag-3' and 5'- tccatcggaagattcgtagc-3', GAPDH 5'- attgccctcaacgaccactt-3' and 5'-ggtccaccaccctgttgc-3', and B-actin 5'- ctggaacggtgaaggtgaca-3' and 5'-aagggacttcctgtaacaacgca-3'.
  • Cpd. AAA, Cpd. BBB, and Cpd. CCC were able to increase the RNA expression levels of p16.
  • SN31439 at the concentration of 0.1 ⁇ M caused the greatest re-expression of p16 over no treatment. Because the higher levels of p16 seemed to have less effect in causing re-expression of p16 there may be some issues with drug solubility or toxicity at the higher concentrations tested.
  • Cell culture-based assays can be used to evaluate the ability of compounds of the invention to inhibit one or more cellular activities, such as cancer cell growth and/or survival.
  • Numerous cancer cell lines can be obtained from the American Type Culture Collection (ATCC) and other sources. Briefly, cells are seeded into 96-well, tissue-culture treated, opaque white plates (Thermo Electron, Vantaa, Finland), at between 5000 and 10000 cells per well, depending on the speed of cell proliferation, in 100 ⁇ l of appropriate growth medium (determined by the ATCC). Cells are then exposed to the appropriate concentration of drug or an equal amount of DMSO (drug diluent) and allowed to grow in its presence for 96 hours.
  • DMSO drug diluent
  • CCG Cell-Titer-Glo

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